13-81895010-A-G

Position:

• chr13-81895010-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.593 in 151,826 control chromosomes in the GnomAD database, including 27,832 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27832 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90043 AN: 151706 Hom.: 27815 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.633

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.593 AC: 90108 AN: 151826 Hom.: 27832 Cov.: 31 AF XY: 0.595 AC XY: 44177 AN XY: 74230

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.636

Alfa AF: 0.655 Hom.: 39614

Bravo AF: 0.590

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7318037; hg19: chr13-82469145;